Code Exercise

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# Assignment 002

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# Examine an OTU Table in R

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- Go to the Human Microbiome Project (HMP): [https://www.hmpdacc.org/HMQCP/](https://www.hmpdacc.org/HMQCP/)

- Examine the datasets available

- Clone the second class repository:  
  [https://github.com/bjklab/EPID674_002_sequences-to-counts.git](https://github.com/bjklab/EPID674_002_sequences-to-counts.git)

- Install & load packages necessary to read the HMP OTU table (included in second class repository)

- View the data & complete a brief assignment

]

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# Using the [rstudio.cloud](https://rstudio.cloud) console

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```r
# install necessary functions 
# (first time only)
# (this will take a while)
install.packages('tidyverse')

# load tidyverse functions
library(tidyverse)
```

]

.pull-right[

- Code at left installs and loads the "tidyverse" package

- The "tidyverse" package includes a set of other packages that permit streamlined data processing

- See Hadley Wickham's _R For Data Science_: [https://r4ds.had.co.nz/](https://r4ds.had.co.nz/)

]

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exclude: TRUE

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```r
# make sure tidyverse loaded
library(tidyverse)

# load (trimmed) HMP V1-V3 OTU table 
# (downloaded with Class 2 repository)
otu <- read_tsv(
  file = 
    "./data/otu_table_psn_v13_TRIMMED.txt.gz",
)

# note: full HMP table crashes rstudio.cloud
# but if you're using your own computer...
#
# otu <- read_tsv(
#   file = "./data/otu_table_psn_v13.txt.gz",
#   skip = 1 # skips an empty first row
# )

# View(otu) # can try "View" in RStudio
otu # show what you've read
```

]

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```
## # A tibble: 43,140 x 22
##    `#OTU ID`    `700110831` `700021898` `700113546` `700016133` `700113545`
##    <chr>              <dbl>       <dbl>       <dbl>       <dbl>       <dbl>
##  1 OTU_97.1               0           0           0           0           0
##  2 OTU_97.10              0           0           0           0           0
##  3 OTU_97.100             0           0           0           0           0
##  4 OTU_97.1000            0           0           0           0           0
##  5 OTU_97.10000           0           0           0           0           0
##  6 OTU_97.10001           0           0           0           0           0
##  7 OTU_97.10002           0           0           0           0           0
##  8 OTU_97.10003           0           0           0           0           0
##  9 OTU_97.10004           0           0           0           0           0
## 10 OTU_97.10005           0           0           0           0           0
## # … with 43,130 more rows, and 16 more variables: 700015293 <dbl>,
## #   700103483 <dbl>, 700097251 <dbl>, 700024697 <dbl>, 700111520 <dbl>,
## #   700038545 <dbl>, 700037298 <dbl>, 700023638 <dbl>, 700016135 <dbl>,
## #   700038435 <dbl>, 700111591 <dbl>, 700109465 <dbl>, 700106547 <dbl>,
## #   700100244 <dbl>, 700114014 <dbl>, Consensus Lineage <chr>
```

]

---

```r
# load (trimmed) HMP V1-V3 OTU table 
# (downloaded with Class 2 repository)
otu <- read_tsv(
  file = "./data/otu_table_psn_v13_TRIMMED.txt.gz",
)
# View(otu) # try the "View" function in RStudio
otu # show what you've read
```

---

```r
# note: full HMP table crashes rstudio.cloud
# but if you're using your own computer...

otu <- read_tsv(
  file = "./data/otu_table_psn_v13.txt.gz",
  skip = 1 # skips an empty first row
)

# View(otu) # try the "View" function in RStudio
otu # show what you've read
```

---
exclude: TRUE

.pull-left[

```r
# make sure tidyverse loaded
library(tidyverse)

# load HMP sepcimen data 
# (downloaded with Class 2 repository)
specimens <- read_tsv(
  file = 
    "./data/v13_map_uniquebyPSN.txt.bz2",
)

specimens # show what you've read
# View(specimens) # also try the "View" function in RStudio
```

]

.pull-right[

```
## # A tibble: 2,970 x 11
##    `#SampleID`    RSID visitno sex   RUNCENTER HMPbodysubsite Description  X8   
##          <dbl>   <dbl>   <dbl> <chr> <chr>     <chr>          <chr>        <lgl>
##  1   700013549  1.58e8       1 fema… BCM       Stool          HMP_Human_m… NA   
##  2   700014386  1.58e8       1 male  BCM,BI    Stool          HMP_Human_m… NA   
##  3   700014403  1.58e8       1 male  BCM,BI    Saliva         HMP_Human_m… NA   
##  4   700014409  1.58e8       1 male  BCM,BI    Tongue_dorsum  HMP_Human_m… NA   
##  5   700014412  1.58e8       1 male  BCM,BI    Hard_palate    HMP_Human_m… NA   
##  6   700014415  1.58e8       1 male  BCM,BI    Buccal_mucosa  HMP_Human_m… NA   
##  7   700014418  1.58e8       1 male  BCM,BI    Attached_Kera… HMP_Human_m… NA   
##  8   700014421  1.58e8       1 male  BCM,BI    Palatine_Tons… HMP_Human_m… NA   
##  9   700014424  1.58e8       1 male  BCM,BI    Throat         HMP_Human_m… NA   
## 10   700014427  1.58e8       1 male  BCM,BI    Supragingival… HMP_Human_m… NA   
## # … with 2,960 more rows, and 3 more variables: X9 <lgl>, X10 <lgl>, X11 <dbl>
```

]

---

```r
# load HMP sepcimen data 
# (downloaded with Class 2 repository)
specimens <- read_tsv(
  file = "./data/v13_map_uniquebyPSN.txt.bz2",
)

specimens # show what you've read
```

```r
# View(specimens) # also try the "View" function in RStudio
```

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# Questions

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- How many OTUs (rows) in the HMP V1-V3 OTU table?

- How many specimens (rows) in the HMP specimen map?

- Which specimen types are included? (try the "View" function)

- Do you see any other OTU tables on the HMP DACC portal?

]

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# Done!
### Post questions to the discussion board!

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# Thank you!
#### Slides available: [github.com/bjklab](https://github.com/bjklab/EPID674_002_sequences-to-counts.git)
#### [brendank@pennmedicine.upenn.edu](brendank@pennmedicine.upenn.edu)